Merge branch 'master' of github.com:openchemistry/avogadrolibs into a…

…dd-msgpack Signed-off-by: Geoff Hutchison <[email protected]>
OpenChemistry · Nov 13, 2023 · a2d876c · a2d876c
2 parents a1e2790 + 13bb1e5
commit a2d876c
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Showing 245 changed files with 46,514 additions and 21,635 deletions.
diff --git a/.github/codeql-config.yml b/.github/codeql-config.yml
@@ -1,3 +1,8 @@
 query-filters:
   - exclude:
       id: cpp/integer-multiplication-cast-to-long
+paths-ignore:
+  - '**/moc_*.*'
+  - '**/ui_*.h'
+  - 'thirdparty/**/*.*'
+  - 'utilities/**/*.*'
diff --git a/.github/workflows/build_cmake.yml b/.github/workflows/build_cmake.yml
@@ -11,10 +11,14 @@ env:
   # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.12
-  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON
+  FEATURES: -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_VTK=ON -DUSE_3DCONNEXION=ON
   CACHE: -DCMAKE_C_COMPILER_LAUNCHER=sccache -DCMAKE_CXX_COMPILER_LAUNCHER=sccache
   SCCACHE_GHA_ENABLED: "true"
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 jobs:
   build:
     name: ${{ matrix.config.name }}
@@ -64,22 +68,6 @@ jobs:
             cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
             cpack: "",
           }
-        - {
-            name: "Ubuntu Leak Sanitizer", artifact: "",
-            os: ubuntu-20.04,
-            cc: "gcc", cxx: "g++",
-            build_type: "lsan",
-            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
-            cpack: "",
-          }
-        - {
-            name: "Ubuntu Thread Sanitizer", artifact: "",
-            os: ubuntu-20.04,
-            cc: "gcc", cxx: "g++",
-            build_type: "tsan",
-            cmake_flags: "-G Ninja -DENABLE_TESTING=ON -DTEST_QTGL=OFF -USE_SYSTEM_ZLIB=ON",
-            cpack: "",
-          }
         - {
             name: "Ubuntu Undefined Behavior Sanitizer", artifact: "",
             os: ubuntu-20.04,
@@ -97,6 +85,7 @@ jobs:
         sudo apt-get -qq update
         sudo apt-get -qq install ninja-build libeigen3-dev libboost-all-dev libglew-dev libxml2-dev 
         sudo apt-get -qq install qtbase5-dev qtchooser qt5-qmake qtbase5-dev-tools libqt5x11extras5-dev libqt5svg5-dev
+        sudo apt-get -qq install libgcc-10-dev libgcc-9-dev
     - name: Install Dependencies (macOS)
       if: runner.os == 'macOS'
       run: |
@@ -110,19 +99,31 @@ jobs:
       run: choco install ninja
 
     - name: Checkout openchemistry
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/openchemistry
         submodules: recursive
 
     - name: Checkout avogadroapp
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadroapp
         path: avogadroapp
 
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: molecules
+
+    - name: Checkout i18n
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/avogadro-i18n
+        path: avogadro-i18n
+
     - name: Checkout avogadrolibs
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: avogadrolibs
 
@@ -137,7 +138,7 @@ jobs:
       uses: jurplel/install-qt-action@v3
       with:
         cache: True
-        tools: 'tools_openssl_x64'
+        tools: 'tools_opensslv3_x64'
         version: ${{ env.QT_VERSION }}
         host: 'windows'
         target: 'desktop'
@@ -196,6 +197,15 @@ jobs:
         done
         otool -L libinchi.?.?.?.dylib
         cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/
+        # finally, fixup the binaries
+        #cd ../bin
+        #for exe in obabel obmm eht_bind genXrdPattern; do
+        #  for libpath in `otool -L ${exe} | grep '/Users/runner/work' | awk '{print $1}'`; do 
+        #    export lib=`echo $libpath | cut -d '/' -f 9`;
+        #    echo "Fixing $exe $lib $libpath"
+        #    install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe
+        #  done
+        #done
 
     - name: Run tests
       if: matrix.config.os == 'ubuntu-20.04'
@@ -249,21 +259,22 @@ jobs:
           fi # certificate exists
         fi # password exists
 
-    - name: Pack
-      if: matrix.config.artifact != 0
+    - name: Create Mac and Windows Packages
+      if: matrix.config.os == 'windows-latest' || matrix.config.os == 'macos-latest'
       shell: bash
       run: |
         if [ -z "${P12_PASSWORD}" ]; then
           unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
         fi
+        [[ ! "${GITHUB_REF}" =~ "tags" ]] && export SNAPSHOT_DATE=`date -j "+%d-%m-%y"`
         cpack ${{ matrix.config.cpack_flags }}
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
         P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: AppImage
-      if: matrix.config.os == 'ubuntu-18.04'
+      if: matrix.config.os == 'ubuntu-20.04' && matrix.config.build_type == 'Release'
       shell: bash
       run: |
         mkdir appdir
@@ -278,27 +289,24 @@ jobs:
         chmod a+x appdir/AppRun
         ./appimagetool-x86_64.AppImage appdir
         mv Avogadro2*.AppImage avogadroapp # for upload
-        # remove the cpack files
-        rm avogadroapp/Avogadro2*Linux.*
       working-directory: ${{ runner.workspace }}/build
 
     - name: Notarize Mac DMG
       if: runner.os == 'macOS'
       run: |
-        # check current directory (failing signing)
-        echo `pwd`
-        ls -ld
         # check if we have the password and the username
         if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then
           codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg
-          npx notarize-cli --file Avogadro2*.dmg
+          xcrun notarytool submit Avogadro2*.dmg --apple-id "$NOTARIZE_USERNAME" --team-id "$NOTARIZE_TEAM" --password "$NOTARIZE_PASSWORD" --verbose --wait
+          xcrun stapler staple -v Avogadro2*.dmg
         fi
       working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
+        NOTARIZE_TEAM: ${{ secrets.AC_TEAM }}
         NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }}
         NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-        PRODUCT_BUNDLE_IDENTIFIER: cc.avogadro
+      continue-on-error: true
 
     - name: Setup tmate session
       if: ${{ failure() }}

diff --git a/.github/workflows/build_m1.yml b/.github/workflows/build_m1.yml
@@ -6,7 +6,11 @@ env:
   # this is different from MACOSX_DEPLOYMENT_TARGET to prevent build problems
   # we set MACOSX_DEPLOYMENT_TARGET later
   MACOS_TARGET: 10.12
-  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF
+  FEATURES: -DUSE_VTK=ON -DBUILD_GPL_PLUGINS=ON -DWITH_COORDGEN=OFF -DUSE_3DCONNEXION=ON
+
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
 
 jobs:
   build:
@@ -37,41 +41,38 @@ jobs:
         fi
 
     - name: Checkout openchemistry
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/openchemistry
         submodules: recursive
 
     - name: Checkout avogadroapp
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadroapp
         path: avogadroapp
 
+    - name: Checkout molecules
+      uses: actions/checkout@v4
+      with:
+        repository: openchemistry/molecules
+        path: molecules
+
     - name: Checkout avogadrolibs
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: avogadrolibs
 
     - name: Checkout i18n
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadro-i18n
         path: avogadro-i18n
 
-    - name: Grab cache files
-      uses: actions/cache@v3
-      with:
-        path: |
-          ${{ runner.workspace }}/build/thirdparty
-          ${{ runner.workspace }}/build/Downloads
-        key: ${{ matrix.config.name }}-thirdparty
-
     - name: Configure
       run: |
         if [ ! -d "${{ runner.workspace }}/build" ]; then mkdir "${{ runner.workspace }}/build"; fi
         cd "${{ runner.workspace }}/build"
-        # won't have any effect except on Mac
         echo "MACOSX_DEPLOYMENT_TARGET=${{ env.MACOS_TARGET }}" >> $GITHUB_ENV
         CC=${{matrix.config.cc}} CXX=${{matrix.config.cxx}} cmake $GITHUB_WORKSPACE ${{env.FEATURES}} -DCMAKE_BUILD_TYPE=${{matrix.config.build_type}} ${{matrix.config.cmake_flags}}
       shell: bash
@@ -87,22 +88,32 @@ jobs:
       working-directory: ${{ runner.workspace }}/build/prefix/lib/openbabel 
       run: |
         for plugin in *.so; do
-          for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do 
-            export lib=`echo $libpath | cut -d '/' -f 9`;
+          for libpath in `otool -L ${plugin} | grep '/Users/runner' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 10`;
             echo "Fixing $plugin $lib $libpath"
             install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin
           done
         done
         cd .. # build/prefix/lib
         for plugin in libinchi.?.?.?.dylib; do
-          for libpath in `otool -L ${plugin} | grep '/Users/runner/work' | awk '{print $1}'`; do 
-            export lib=`echo $libpath | cut -d '/' -f 9`;
+          for libpath in `otool -L ${plugin} | grep '/Users/runner' | awk '{print $1}'`; do 
+            export lib=`echo $libpath | cut -d '/' -f 10`;
             echo "Fixing $plugin $lib $libpath"
             install_name_tool -change $libpath @executable_path/../Frameworks/$lib $plugin
           done
         done
         otool -L libinchi.?.?.?.dylib
         cp -p libinchi* ../Avogadro2.app/Contents/Frameworks/
+        # finally, fixup the binaries
+        #cd ../bin
+        #for exe in obabel obmm eht_bind genXrdPattern; do
+        #  for libpath in `otool -L ${exe} | grep '/Users/runner' | awk '{print $1}'`; do 
+        #    export lib=`echo $libpath | cut -d '/' -f 10`;
+        #    echo "Fixing $exe $lib $libpath"
+        #    install_name_tool -change $libpath @executable_path/../Frameworks/$lib $exe
+        #  done
+        #done
+
 
     - name: Install the Apple certificate
       # From GitHub docs: https://docs.github.com/en/actions/guides/installing-an-apple-certificate-on-macos-runners-for-xcode-development
@@ -138,39 +149,38 @@ jobs:
             # signing occurs via avogadroapp cpack instructions
           fi # certificate exists
         fi # password exists
+        # remove any previous DMG in case they're still around
+        rm -f avogadroapp/*.dmg
 
-    - name: Pack
-      if: matrix.config.artifact != 0
+    - name: Create Mac and Windows Packages
       shell: bash
       run: |
         if [ -z "${P12_PASSWORD}" ]; then
           unset CODESIGN_IDENTITY # to prevent cpack failing when trying to sign
         fi
+        [[ ! "${GITHUB_REF}" =~ "tags" ]] && export SNAPSHOT_DATE=`date -j "+%d-%m-%y"`
         cpack ${{ matrix.config.cpack_flags }}
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
         P12_PASSWORD: ${{ secrets.P12_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: Notarize Mac DMG
       if: runner.os == 'macOS'
       run: |
-        pwd
-        ls -l
         # check if we have the password and the username
         if [ -n "${NOTARIZE_PASSWORD}" ] && [ -n "${NOTARIZE_USERNAME}" ]; then
-          echo "codesign DMG"
           codesign -s "$CODESIGN_IDENTITY" --timestamp Avogadro2*.dmg
-          echo "notarizing"
-          npx notarize-cli --file Avogadro2*.dmg
+          xcrun notarytool submit Avogadro2*.dmg --apple-id "$NOTARIZE_USERNAME" --team-id "$NOTARIZE_TEAM" --password "$NOTARIZE_PASSWORD" --verbose --wait
+          xcrun stapler staple -v Avogadro2*.dmg
         fi
+      working-directory: ${{ runner.workspace }}/build/avogadroapp
       env:
+        NOTARIZE_TEAM: ${{ secrets.AC_TEAM }}
         NOTARIZE_USERNAME: ${{ secrets.AC_USERNAME }}
         NOTARIZE_PASSWORD: ${{ secrets.AC_PASSWORD }}
         CODESIGN_IDENTITY: ${{ secrets.CODESIGN_ID }}
-        PRODUCT_BUNDLE_IDENTIFIER: cc.avogadro
       continue-on-error: true
-      working-directory: ${{ runner.workspace }}/build/avogadroapp
 
     - name: Upload
       if: matrix.config.artifact != 0

diff --git a/.github/workflows/build_wheels.yml b/.github/workflows/build_wheels.yml
@@ -2,6 +2,10 @@ name: Build Wheels
 
 on: [push, pull_request]
 
+concurrency:
+  group: ${{ github.workflow }}-${{ github.ref }}
+  cancel-in-progress: true
+
 env:
   # Don't build python 2.7, pypy, or 32-bit wheels or Mac arm64 on Py3.8
   CIBW_SKIP: "cp36-* cp37-* cp311-* cp38-macosx_arm64 pp* *-musllinux_* *-manylinux_i686 *-win32"
@@ -42,7 +46,7 @@ jobs:
         os: [ubuntu-20.04, macos-latest, windows-2019]
 
     steps:
-      - uses: actions/checkout@v3
+      - uses: actions/checkout@v4
         with:
           # Grab the whole history so that setuptools-scm can see the tags and
           # give it a correct version even on non-tag push.

diff --git a/.github/workflows/clang-format-check.yml b/.github/workflows/clang-format-check.yml
@@ -10,7 +10,7 @@ jobs:
     - name: 'Install clang-format'
       run: sudo apt-get -qq install clang-format-13
 
-    - uses: actions/checkout@v3
+    - uses: actions/checkout@v4
 
     - name: 'Run clang-format-diff'
       run: |

diff --git a/.github/workflows/clang-tidy.yml b/.github/workflows/clang-tidy.yml
@@ -41,19 +41,19 @@ jobs:
         version: ${{ env.QT_VERSION }}
 
     - name: Checkout openchemistry
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/openchemistry
         submodules: recursive
 
     - name: Checkout avogadroapp
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         repository: openchemistry/avogadroapp
         path: avogadroapp
 
     - name: Checkout avogadrolibs
-      uses: actions/checkout@v3
+      uses: actions/checkout@v4
       with:
         path: avogadrolibs
         fetch-depth: 2

diff --git a/.github/workflows/codacy.yml b/.github/workflows/codacy.yml
@@ -28,15 +28,18 @@ permissions:
 
 jobs:
   codacy-security-scan:
+    name: Codacy Security Scan
     permissions:
       contents: read # for actions/checkout to fetch code
       security-events: write # for github/codeql-action/upload-sarif to upload SARIF results
-    name: Codacy Security Scan
     runs-on: ubuntu-latest
+    concurrency:
+      group: ${{ github.workflow }}-${{ github.ref }}
+      cancel-in-progress: true
     steps:
       # Checkout the repository to the GitHub Actions runner
       - name: Checkout code
-        uses: actions/checkout@v3
+        uses: actions/checkout@v4
 
       # Execute Codacy Analysis CLI and generate a SARIF output with the security issues identified during the analysis
       - name: Run Codacy Analysis CLI